You have to bear in mind that the 60mm stroke will increase the transfer and exhaust timings and decrease the inlet, on a piston port motor, though the inlet should be 360 degrees on a reed valve kit. Run the same figures through the calculators with a 58mm stroke and you'll see what I mean.
You've added a 110mm rod which gives you some flexibility to adjust the timings by the use of different packers, 3mm ought to put you back where the kit designer intended but factor in the extra stroke and you end up with the piston out the top. Level is 0, out would be -1 or whatever you actually measure.
If you're now level at TDC, and just below at BDC then you're close. IMO you have now to look at the head gasket as the only thing you now have to play with. Pack the base up further and you end up with the piston further down at BDC.
An adult may be along shortly to elaborate
